End of All Harmony
by draconichero21
Summary: On a stormy evening, Twilight is visited by a weary, injured Princess Luna who tells Twilight that her mother, Queen Nebula has returned. The high queen is nothing like her two daughters and is evil to the core and she has taken over Equestria. Do Twilight and friends have the power to stop her? T for violence as a safety net.
1. The Return of Queen Nebula

**(A/N: Much like my fanfic The Very Special Lesson, this was another idea I had for what I thought of when I tried to think of what the plot to a My Little Pony Friendship Is Magic Movie might be like. If the studio was going to make a movie though I'd prefer they do one using the plot to The Very Special Lesson, but that's only because this plot is a lot darker and edgier compared to the standard MLP plot and is more brony friendly. Still it's nothing that couldn't be aired on TV, either fic. So sit back, relax, and enjoy. Oh and this was made to exist AFTER the season 3 premiere so any continuity after Season 3, episode 2 does not hold water for this fanfic. It's just easier that way for the ideas I have in mind, especially since I directly contradict canon in someplaces *cough*Discord*cough*).**

Disclaimer: My Little Pony Friendship Is Magic belongs to Hasbro and Lauren Faust

* * *

**Ponyville, Night**

A bad storm was currently blowing through Ponyville. Harsh winds blew and heavy rain poured, keeping all Pegasi grounded, not that any were even outside. All ponies were inside and the storm was only getting worse. Twilight Sparkle, knowing the dangers, was currently reinforcing the library, since it was made out of an oak tree. As part of her reinforcements, she asked Spike to go and remove something that was hanging out on the tree branch outside her bedroom window, while she continued to put up magic wards along the inside of the library.

As Spike opened the window though, a fierce wind blew into the library, sending books, other items and Spike hurtling through the air. Twilight responded quickly by shutting the window with magic and catching Spike before he landed. She then placed her friend on the ground and put up a magic wall alongside the bedroom area so the wind wouldn't blow into the rest of the library if the window opened again. She retrieved the object hanging out on the branch and put it in its proper place. She then stood in the middle of the library, concentrated and projected a large barrier to surround the entire library.

"There," she said, "That should protect the library until this storm blows over."

A crack of thunder sounded through the air. It was so loud that a Dragon's Roar would've been quieter.

"Man, listen to that," Spike jerked his thumb at the flash of lightning that followed. "I didn't know Ponyville could get storms this bad."

"Any place can get a really bad storm, Spike," Twilight said as she began to pick up the books that had fallen from when Spike opened the window, "The important thing is to know how to survive in one." Twilight lifted a book open on the table, "And this 'How to Survive in Bad Weather' book is the key to our safety." Twilight smiled proudly and strutted to put the book back on its proper shelf, "This library is completely protected, both from lightning and from the wind."

As Twilight began to put the book back, outside in Ponyville, the silhouette of another pony approached the library. For what reason they were braving the storm was unknown, but soon would become abundantly clear. With magic they opened a small hole in Twilight's barrier and then closed it back up behind them.

Twilight put all the books back on their proper shelves and looked around to make sure the library floor was clean. "There, perfect."

A knock to her door alerted her. "Company? In this storm?" She opened the door. A flash of lightning concealed the identity of the pony that had come knocking at the door, but upon entering the library the library the identity of the individual was many unmistakable.

"Princess Luna?" Twilight gasped. The alicorn stood before Twilight, but she did not look well at all. One of her eyes was closed, her coat was mangled and she looked woozy. Her wings were not folded and bent a little and her crown was missing. Her mane was split in several locations and with every step she took it seemed like she was threatening to fall over.

Luna barely made it into the center of the library, with Twilight too shocked to speak, wondering what could've possibly happened to Luna in the first place. Luna opened her mouth and even with tremendous effort, barely managed to get out: "Twilight…Sparkle…help," before collapsing in a heap on the library floor.

"PRINCESS LUNA!" Twilight exclaimed.

Luna eventually came to and by the time she did she found herself in Twilight's bed with a cool pack and bandages. Each of Twilight's friend's had braved the storm and all of them had now arrived at the library. Rarity was wearing a very fancy rain jacket, Applejack and Rainbow Dash were currently sharing a towel to dry off from the harsh storm, and Fluttershy was cowering as she curled up in a blanket. Pinkie Pie meanwhile was wearing a snorkel, deep sea diving goggles and flippers as well as an inner tube.

"Twilight, I think she's waking up," Spike called to her as the ponies all assembled by the fallen Princess.

"Twilight Sparkle," Princess Luna groaned upon seeing the faithful student of her sister at her bedside.

"Princess Luna, what happened, what's going on?" Twilight asked in deep concerned.

"She's come back," Luna said in a low voice.

"Who's come back?" Twilight asked with growing curiosity.

"Our mother," Luna stated, "Queen Nebula."

"I don't understand," Twilight was confused.

"Twilight our mother…is not like my sister and me. She is…truly evil."

"Evil?" Twilight was greatly confused.

"Listen to me and listen to me well, Twilight Sparkle. You must understand what has happened…

* * *

**Earlier…**

Dusk was reaching Canterlot as Luna was just waking up for the evening and Celestia was getting ready to lower the sun. However, an unexpected guest had arrived at the royal city and was about to change what would have been considered an otherwise normal day in tri-stable area. It was an Alicorn with a turquoise coat and eyes and a crimson, flashy mane and tail, much like Equestria's co-ruling monarchs. On the ankles of her hoofs she wore glass shoes matching her mane with tufts of ethereal energy swirling about her feet. Her cutie mark was that of a black hole. She had olive green eyes and walked along the grass with a sense of grace and poise. The ponies all around her began whispering to each other wondering who she was. Many had not seen her before, though that was understandable. This alicorn had not set foot in Canterlot since before Discord's reign.

However, as she approached the gates of the palace she activated a magic spell and conjured up the Canterlot royal seal. The guards looked into the eyes of the Alicorn bearing down upon them and were stunned. "Y-your majesty." Instantly they subsided and let the Alicorn pass, who made her way to the throne room.

Seeing this, one of the lookouts ran for Celestia's chambers and bolted into the room. "Your majesty, Princess Celestia, her majesty…Queen Nebula has returned to Canterlot."

Celestia gasped and was shocked for a moment, but quickly gained her composure. "Fetch my sister and clear the chambers," she ordered.

"Yes your highness."

Celestia's mother entered the throne room, prying the doors open with magic as her horn glowed crimson.

"Mother, what are you doing here?" Celestia asked, walking towards her.

"I thought I'd come and check up on how my little girl is doing. How long has it been Celestia, one thousand years? Two thousand maybe? It's been so long I've simply stopped counting the years."

The sound of clopping echoed from the hallway as Luna bolted into the room. "Tia, I heard the news and I—" She saw the turquoise Alicorn standing before her and Celestia and skidded to a halt, gasping. "Mother?"

"Ah, good evening to you to, Luna my dear," Nebula smiled at her.

"Mother, is everything all right? I know we haven't seen each other, but I've sent you letters," Celestia was very concerned. Her mother was supposed to be in retirement on a sunny beach far from Canterlot on the Southeastern side of Equestria.

"It's the strangest thing," Nebula said as she approached the throne, "I was trying to recall the other day how and why I left the reign of Equestria to you, Celestia, or even Luna. And then I remembered something," Nebula stood in front of the throne and looked over her shoulder. Her olive green eyes turned bright red. "I didn't." Nebula turned around and flapped out her wings. Her horn shined with magical energy as powerful waves of dark energy resounded from her general area, shattering a few of the windows and shoving Luna and Celestia towards the other side of the room. Casting another spell, Nebula transformed the room tiles and walls to be a dark, blood red. Celestia's throne room went from looking harmonious and delicate to intimidating and demonic. Nebula's form had also changed and she now was wearing Crimson armor and took a form very similar to when Luna was Nightmare Moon only the queen's color scheme was the one that was currently taking up a large portion of the room at the moment.

"B-But…that's impossible," Luna gaped.

"You two have been very bad, usurping the throne from your mother," Nebula said stepping towards Luna and Celestia, "It's high time I took back what belongs to me."

Celestia's eyes converged. "Mother, Equestria is mine now. You are the one usurping."

"Is it usurping to overthrow a usurper? Equestria knows her queen and yearns for her return." Nebula approached Luna and Celestia and slammed the door, cutting off their only means of escape except through the broken windows. "When last you two defied me, I gave you the option to either be banished from the castle, or be physically punished. This time," Nebula's eyes turned blank white with powerful magical energy, "I will not give you that choice."

Dark waves of energy blasted outward from Nebula's horn, making it hard for Luna and Celestia to remain on their feet as the pressure of the waves caused by their mother's ungodly power caused them to stagger.

With all her might, Celestia fired a beam of magical energy at her mother. Nebula blocked with a spherical barrier. Luna tried her hand as well, but her attack was met with the same result. Nebula unleashed a blast wave of red energy to attack her daughters, knocking them into the wall for the second time and causing them to drop to their knees, but both got back up. Celestia charged at her mother extended a constant yellow beam off her horn, locking it with her mother's red one.

"You've improved Celestia. Last time we clashed, I destroyed your magic saber within an instant."

"How did you come back? You shouldn't remember anything at all!" Celestia exclaimed, frowning.

"Why don't you ask that faithful student of yours?" Nebula chuckled darkly.

"What are you talking about?"

Nebula was about to respond but flapped and dodged out of the way as Luna tried to sneak attack on her from above and behind. With a teleportation spell, Nebula pounced on her younger daughter from above, sending her into the floor.

With a flash of energy, Celestia's mane and tail ignited and she flapped into the air and fired off a burst of flame with a single flap of her wings, smashing it into her mother's body, but barely managing to make any sort of impact.

By the time Celestia realized it, Nebula was behind her. Her mother attacked her by jamming her horn into Celestia's hindquarters and electrifying her horn. Celestia was zapped harshly and hit the ground.

Luna rose triumphantly back up to face off against her mother once again. She created a ball of blue lightning with her horn and attacked her mother head on.

Nebula kicked it back at Luna with her hind legs. Luna did the same and returned her attack again. This exchange continued, like a game of tennis, until Luna kicked with such force that Nebula didn't react in time and took the attack to the face. She was thrown backwards, head over hooves, but flapped out her wings to steady herself in midair. Shaking off the disorientation she prepared to strike again, but Celestia was back in the air and conjured up several fireballs. She then launched them all at Nebula with varying trajectories.

The former queen conjured up a small black hole and sucked all of the fire into it, dissipating it. She then dispelled her small tear in the space-time continuum.

"Try this!" Luna declared. Her horn flashed light blue and a beam of ice went sailing towards Nebula. She conjured up the black hole from earlier and used the fire she had sucked into to counter Luna's ice beam. Then with a midair stomp of her hooves, she sent out an aerial tremor, creating more dark waves. The pressure of these waves sent Luna and Celestia hurtling through the air. Both princesses steadied themselves with their wings as Nebula had done before.

With magnificent speed, Nebula charged and then bucked Celestia's right side and blasted Luna with a beam of energy from behind, sending them both into the ground. She landed upon the ground. "Give up, Celestia, Luna. You know it pains me to hurt you."

"We," Celestia rose to her feet, "will never give up." With a fierce war cry she charged at her mother, but with a telekinesis spell, Nebula whipped Celestia completely to the other side of the room, knocking her on her side as Celestia crumpled to the ground in pain as a shard of glass disloged from the broken window and landed upon her body. Thankfully it landed flatly and did not stab into Celestia's skin.

Luna tried to stand, but was too injured to get up. Nebula looked at her and approached slowly. "Wittle Bitty Luna, my second daughter. Such potential you showed, such high hopes I had for you, but you've dashed those hopes of mine and once again stand by your sister against me. I'm afraid I cannot take the risk you would betray me again." Nebula's horn glinted gray. "Farewell."

It all happened so fast, Luna didn't know what had happened until it was far too late. In an instant, Celestia stood between Nebula and Luna and the attack meant for Luna hit Celestia instead. When the bright flash before her eyes cleared, Luna saw what had become of her older sister. Celestia had been turned to solid stone. Her form was majestic and calm. She had come between her mother and sister, facing her mother's attack without backing down, not moving an inch from Nebula's attack. She had protected her sister with her very life.

Luna's eyes trembled. Without Celestia to aid her, the battle was as good as lost. She had no choice. She had to leave Canterlot to gather reinforcements and she knew just who to get. Luna smashed an unbroken window near her with her magic and flew out of it only to see that Nebula had managed to completely transform Canterlot into a town much like the throne room. It was disharmony on a grand scale the likes of which Luna had never expected—or wanted—to see again. Much unlike Discord though, this was organized disharmony and all of the ponies in Canterlot were affected.

"Seize her! The princess of Canterlot seeks to betray her country!" Nebula shouted, sticking her hoof out the window.

Luna took to the skies towards Ponyville. She had to escape her mother's dark tyrannical reign.

"Don't think you can escape from me, Luna dear," Nebula said and arched her back before sticking her chest proudly forward and conjuring up another spell, creating a fierce storm, the fiercest that any city in Equestria had seem in quite a long time. The winds knocked Luna far off course, throwing her about like a rag doll. Lightning struck her three times and it was absolute heck getting out of Canterlot. Luna collapsed once already when she was blasted out of the air by a bolt of lightning, but she came to almost immediately. When she awoke, she realized she was in ponyville just outside city hall. She then got up on her shaking legs and braved the harsh rain and wind towards the library.

* * *

**Present Time**

"And," Luna coughed, "you know the rest."

"I don't understand," Twilight said, with her ears bent down, "Why is your mother doing all of this?"

"Our mother was a disharmonious individual. You…" Luna coughed.

"Don't worry princess," Twilight said with a confident expression, "We'll stop Queen Nebula and put Equestria back to the way it was. Come on girls," Twilight said dashing away towards the basement to get the elements of harmony that she kept in a brief case behind several magic wards. Celestia had given them to her for safekeeping after the Chrysalis incident. In the likely event that Twilight would need the Elements of Harmony again, she figured it was best Twilight hold onto the elements rather than leaving them in Canterlot and so that if the town got taken over, Twilight had the option to retreat rather than sneaking around the castle.

"Twilight…wait…" Luna reached out to her, but found her strength failing her. "Don't…go…" she fainted.

* * *

**Canterlot**

It was an absolute hazard braving the storm back to Canterlot. Thankfully Twilight's magic ward managed to hold up until she was within teleportation distance to bring her friends to Canterlot. However, Canterlot was not what she expected at all. The entire town looked like the apocalypse had just rolled in with buildings demolished and streets on fire. Posters of Nebula's head, looking down at the pony reading it with a caption of 'Obey' were seen all throughout the streets.

The mind controlled guards and soldiers were chasing ponies through the streets. Other ponies were in chains and shackles being ordered into a factory, single file while other ponies were pushing rocks around.

"How horrible!" Fluttershy gasped.

"This is simply dreadful," Rarity added.

"We have no time to lose. We have to make for the palace and fast." Twilight stated.

"Couldn't we just teleport into it?" Applejack asked.

"Princess Celestia's palace is always protected with magic wards to prevent instant teleportation inside, to keep out thieving unicorn ponies. We have to get there the hard way. Come on girls," Twilight began galloping forward. She and the others made their way towards Nebula's castle and burst into the foyer, where upon the queen was waiting for them. She was outside of her combat armor that she had used to fight Luna and Celestia.

"Ah, Twilight Sparkle and her friends," Nebula said as the six ponies glared at the turquoise mare. "I've heard so much about you. And those must be the elements of harmony," she noted the amulets around the necks of Twilight's friends and the tiara upon Twilight's head.

"Queen Nebula, turn Princess Celestia back this instant!" Twilight demanded.

"You barge into my palace and demand things out of me. I thought Celestia taught you better than that."

"We have the elements of harmony. I'm trying to settle this peacefully," Twilight said with a scowl.

"So I see," Nebula said with a smirk. "Well then," she fanned out her wings and smiled. "Hit me with your best shot," she pointed to the center of her chest with the tips of her wings, "Fire away."

"Then you leave us no choice." As they had done twice before, Twilight and her friends summoned the powers of the elements of harmony and blasted Nebula with the power of friendship. However, when the shining nova of friendship power dissipated, Nebula was sitting down, filing her hoof. Twilight's jaw dropped. "H-huh? B-but…?"

"Oh…was that it?" Nebula asked.

"I…I don't understand. It worked on Discord…it worked on Nightmare Moon…"

"Yeah, why don't the Elements of Harmony work on you? You cheater!" Rainbow Dash shouted pointing at the queen with her hoof.

"You've got a lot of guts to say such slanderous words to a queen," Nebula said with a cruel smirk. "But I don't have to explain anything to you. Goodbye bearers of the elements of harmony." Waves of Dark energy exuded outward from Nebula, creating an ocean-like pressure on the six ponies. Rarity screamed in her displeasure from the rumbling. Fluttershy cowered. Twilight watched as best she could as she then saw the five black necklaces and one black tiara Nebula was summoning as they began to circle around her like rotating planets. Twilight tried to conjure up some sort of defense, but in the next instant Nebula unleashed a powerful dark magic attack that sent Twilight and her friends flying into the wall of the entry way and shattering the elements of harmony into tiny pieces. Nebula then walked down the stairs to finish Twilight off as she blacked out.

When Twilight came to though, she was back at the library, in her bed. Cadence was standing over her. "C-cadence?"

"Oh Twilight, thank goodness you're all right."

"What happened?" Twilight groaned.

"You got your flank handed to you that's what happened. Luckily Princess Luna was able to contact Cadence and I and we made it in time to save you and your friends before Nebula made you part of her rock garden." Shining Armor's voice was unmistakable as he came into Twilight's view.

"My great aunt was just so powerful. Even with my love magic, she refused to yield," Cadence frowned.

"You all right Twili?" Shining Armor asked her.

"I'm fine, but…the elements…they didn't work."

"Yes, we heard from your friends," Cadence replied, "Princess Luna said she would explain when you awoke. Come on."

"How is Princess Luna?"

"Better, I applied some first aid to her. She will recover," Cadence explained. "Now come."

Twilight followed her brother and sister-in-law to the basement of the library where Luna was waiting with Twilight's friends. "Ah and here she is at last," Luna said, regarding Twilight, "We've been waiting for you, Twilight Sparkle."

"Luna, what happened? Nebula's magic was so powerful and the elements of harmony didn't work."

"I know, they didn't work. I tried to tell you that." Since Luna was no longer a Canterlot Princess, what with her mother having taken over, she was slipping into more informal speech.

"But…why?"

"I did not finish telling you my story, Twilight Sparkle. When our mother was in power, she wielded a powerful source of magic known as the Elements of Disharmony, though Celestia and I did not discover her source until much later."

"What do you mean?"

"When our mother was in power, Celestia and I were very young. At one point we bravely defied her and told her to stop torturing all the citizens of Equestria and ruling with such an iron fist. Our mother was unhappy with our outright defiance, but she was still our mother so she gave us a choice. We could either be banished from the castle for an undefined period of time or we could be physically punished. Celestia chose banishment for us both. I asked her why and she brought us to the Everfree forest, upon which she introduced me to Discord."

"Whoa, whoa, wait, back up!" Twilight exclaimed, shaking her head violently back and forth before exclaiming, "Celestia and Discord had a history?"

Luna nodded. "Before our mother rose to power, Discord was my sister's friend. She would often sneak away from the castle to go see him. So, when the options were presented to us, she wanted to be banished so she could ask for his help. Discord was a powerful magic user, she believed he had the power to stand up to our mother and he was the one who gave her the courage to stand up to our mother in the first place. With Discord's power aiding us we were able to inflict a powerful amnesia spell upon our mother, robbing her of her memory and turning her into the opposite of what she was, much like you all experienced during the last time Discord roamed free."

"And this is when Discord came to power?" Twilight asked.

"Yes," Luna nodded, "Though Celestia and I had been the ones to defeat our mother, it was Discord who ultimately played the pivotal role and the citizens were practically begging him to take the throne in place of our mother, especially since Celestia and I were too young and inexperienced." Luna looked at the ground in shame, "Stupid, stupid thing to do."

"Princess Celestia said you two discovered the Elements of Harmony to defeat him."

Luna nodded again. "My sister is right. You see, Discord was an okay ruler when he first took to the throne, but much like our mother he abused his authority and he drove everypony mad with his chaos and tyrannical reign with no one to stop him. It took me a while, but I managed to convince Celestia that it was time to say goodbye to her friend. Through research we were able to discover the source of our mother's power and learn of its equal and opposite power: The Elements of Harmony. Since Discord was using the disharmonious elements for his own power we were able to banish him with these elements."

"But I don't understand, if it worked on Discord…"

"Discord was utilizing the elements, but not empowered by them. Nebula is a powerful alicorn so not only can she wield the elements of disharmony, but she can bring out their greatest assets to make her even stronger, therefore the elements of harmony not only will not work on her, but they will simply cancel out her disharmonious elements. However, as you are an inexperienced unicorn, compared to Nebula your power was insufficient to make a complete cancelation," Luna explained.

"One thing still bothers me though," Applejack spoke up, "If y'all used yer fancy magic to mess with the queen's head why didn't she come back to power after Discord was sealed up?"

"An excellent question, fairest Applejack, but one with a simple answer. When Celestia and I sealed Discord we were selective in how we sealed him, leaving that one spell that he cast upon our mother, active, when we purged from the world all he had wrought. It is how he escaped from simple in-fighting caused by three young fillies. However, Twilight Sparkle, when you sealed him, you reset everything, including that spell. Eventually our mother's memory slowly returned and as you can see, she has struck back."

"What do we do then? You're not going to suggest we unseal Discord again are you?"

"That would be the simplest solution," Luna stated.

"But if he breaks out, without the elements of harmony we can't reseal him," Twilight told her.

"One problem at a time, Twilight Sparkle," Luna told her.

"There has to be another way," Cadence spoke up.

Luna thought it over. "Hmmm, there might be."

"Just tell us what we have to do," Twilight stated.

"The jewels of which the Elements of Harmony were crafted from originate from large crystals in the other kingdoms besides Equestria. Perhaps if we revisit these crystals and create a resonance between them, we can restore the Elements of Harmony to a greater state and overpower my mother, defeating her once and for all."

"So we would essentially have to take a trip around the world that means."

"Awww yeah! Road trip!" Rainbow Dash cheered.

"It's not a trip, rainbow one, it's more of a quest, a quest that will test you to your greatest limits," Luna told the young ponies.

"Oooh!" Pinkie Pie exclaimed and ran off out of sight. She came back in two seconds wearing a green tunic and wool cap, carrying a shield and sword on her back with a blue parasprite floating next to her.

"Not that kind of quest Pink one."

"Aww," Pinkie Pie sad sadly as she put her head down.

"Ummm, what are the other kingdoms?" Fluttershy wanted to know.

"As far as I remember the six kingdoms are as follows: the Buffalo Kingdom, keepers of the Crystal of Honesty, the Griffon Kingdom, keepers of the Crystal of Laughter, the Zebra Kingdom, keepers of the Crystal of Kindness, the Dragon Kingdom, keepers of the Crystal of Loyalty, and our kingdom, Equestria are the keepers of the Crystal of Generosity."

"What about the keepers of the Crystal of Magic?" Twilight asked.

"As far as we know that kingdom fell long ago. We know where the Crystal resides, but we believe it is best to save it to last."

"Why?" Twilight asked.

"It is in a difficult place. You will understand when we arrive. For now, we must leave at once. If we rest until morning it will not be safe in Ponyville."

"But where can we go?" Twilight asked.

"If one of the kingdoms is the Buffalo kingdom, we should go to Appleoosa," Applejack stated with a serious look. "Chief Thunderhooves might be able to point us in the right direction."

"Great idea Applejack!" Twilight exclaimed.

"What should we do?" Cadence asked.

"Return to the crystal kingdom," Luna told her. "Our mother will try to overtake every surrounding land in Canterlot starting with the tri-stable area. She will eventually strike your kingdom when she finds out Sombra is no more. If you can defend it from her, it will buy us some time."

"Understood," Cadence stated. She began to head up the stairs.

Before doing the same, Shining Armor went over to Twilight. "Be careful out there Twili."

"You too big brother," she told him. The two nuzzled each other and then Shining Armor followed Cadence up to ground level and out of the library.

"Come my little ponies," Luna said walking in front of Twilight and encouraging her and her friends to head up the stairs, "Our adventure awaits."

With that, while Shining Armor and Cadence made their way back to the Crystal Kingdom, Twilight and her friends headed out towards Appleloosa to rendezvous with the Buffalo. A dangerous journey had begun. A journey to save Equestria from its original, tyrannical queen was underway.

* * *

**Meanwhile…**

In the middle of her newly restored palace, Nebula circled around her stone statue of Celestia. "Ah that was so brave of you, Celestia to protect your sister like that, but of course, I expected nothing less of you." Nebula's horn flashed white. "I could leave you petrified, but of course, I have other uses for you for the time being." Celestia was encased in Nebula's spell and slowly the magic surrounding her began to peel away.

**To be continued…**

* * *

**(A/N: So yeah Nebula is essentially the Evil Queen. If you guys couldn't tell already, for those of you that watched the show, part of this chapter, and other parts of the story, borrow from Codename: Kids Next Door: Operation Z.E.R.O. But yeah now the mane six are off on a quest to fully restore Equestria and stop its tyrannical queen from ruling it with an iron hoof. For those curious the Elements of Disharmony and their harmonious counterparts are: Hatred/Kindness, Betrayal/Loyalty, Deceit/Honesty, Greed/Generosity, Seriousness/Laughter, and Dark Magic/Magic. Okay yeah that last one is kind of a cop-out, but hey it is what it is. Will the mane six be able to save Equestria from Nebula's grasp? And just what twisted plot does the high queen have in store for her daughter? Find out in the next chapter of End of All Harmony).**


	2. The Trial of Honesty

**(A/N: I…I got nothing)**

Disclaimer: My Little Pony: Friendship is Magic © Lauren Faust and Hasbro

* * *

**On the road to Appleoosa**

Because of the storm and the time of night, there were no ponies operating the train station, but that wasn't going to stop Twilight, Luna or the others. Using her magic, Luna enchanted the train to allow it to fly and the ponies were now on their way to Appleoosa, though the journey, as they all knew, would be quite a while, even by the speed they were going at.

Upon settling down on the train and leaving Ponyville behind, the sky turned from red to its normal dark blue as Twilight and her friends now found themselves beyond Nebula's clutches and well into safety.

Twilight went over to the window and looked out as she saw Ponyville vanishing in the distance as the train climbed higher and higher into the air, guided by Luna's magic. She put a hoof upon the glass as she worried for her brother and sister-in-law as well as her parents and all the other ponies she cared about in the tri-stable area.

Luna approached Twilight from behind with a concerned, but reassuring expression. "Twilight, there is nothing we can do for them by staying behind. We have to press forward. It is the only way. If we can defeat Nebula things will go back to how they were."

"I know…but…"

Luna draped her wing over Twilight. "I know you're upset about your failure, but we will fix this. Mistakes can be corrected."

Two tears splashed from Twilight's face, but she understood what Luna was trying to say. She then appeared tired and let out a big yawn.

"You should get some rest, Twilight Sparkle. I am the Princess of the night; I can guide this train straight on through until we can safely land. I will wake thee in the morning."

"Thank you, Princess," Twilight said with a comforted smile.

Luna watched Twilight go to the back of the train to settle down in one of the beds as she walked herself towards the conductor's cabin. She looked out over the horizon as she herself found it impossible not to worry about Canterlot and the rest of Equestria. She still couldn't get over how Celestia had protected her from harm. Luna didn't know if that was just Celestia being her usual sisterly self, if she was making up for when Luna became Nightmare Moon, or if she had meant for Luna to go to Twilight Sparkle and her friends instead of her. Whatever the case, it didn't matter to Luna.

"Tia, it should be you here, not me." She looked up at the Equestrian moon and how it glowed over the horizon. "You are Twilight's teacher, you are the greater ruler. I cannot guide her the way you can. Why did you save me? Why Tia, why?" Luna was shouting as though she thought the moon would answer her. Irritated, Luna tore her eyes away from the sky and looked down over the horizon so that she could guide the enchanted train towards Appleoosa to where the Buffalo roam.

* * *

**The Next Morning**

When Twilight and the others woke up, the train was on the ground, having come to a complete stop. Twilight couldn't find Luna in any of the beds so she wandered the train straight to the conductor's cabin where upon she found Luna curled up on the ground, snoring and whinnying loudly. Twilight looked out the window to see that the sun was high up in the sky. Today marked the start of her and her friends' journey. With vigor in her eyes she silently vowed to save Celestia and all of Equestria.

She then looked down at Luna with a much harsher expression and poked the Equestrian princess with her hoof. "Princess Luna, wake up."

Luna snorted from the sudden prodding as one would if startled in their sleep. She then slowly opened her eyes to the glow of the sunlight. She yawned loudly and got up on all fours as she arched her back like a cat before settling down and shaking out her mane. She then blinked a few more times. "Twilight? Is something the matter?" She then noticed the sunlight. "Daytime? Did I fall asleep?"

"You did, is that bad?" Twilight asked.

Luna tensed her legs and looked at the ground. If she had toes she'd be curling them. If the sun had risen upon its own and Luna had fallen asleep during the night then it meant their mother now had complete control over the lunar and solar cycle, turning Luna back to a crepuscular creature. "It's nothing," Luna responded. "Let us gather the others."

In a few short minutes the seven ponies, and Spike, were outside the train and out on the desert by near where they had first met Chief Thunderhooves and the other buffalo.

"So should we march straight on towards Appleoosa or should we be lookin for them buffalo like a needle in a haystack?" Applejack asked.

"There's no need," Luna stated, "During the night I visited the Chief in his sleep in the realm of dreams…before I fell asleep. He should be joining us shortly with the rest of the herd."

Then, like the sound of distant thunder, a plethora of hooves could be heard in the distance as a dust cloud began to form. The buffalo were charging towards Luna and the others and stopped at a prominent distance from her, Twilight and the others.

"Princess Luna, so it is true what you said," the bulky chief said, stepping forward.

"Indeed, what you experienced the night before was no mere dream as you now see," Luna responded.

"Chief," Applejack stepped forward, standing front and center in front of the others, "We'd be awfully grateful if you could help us. If that Queen Nebula ain't stopped then all of Equestria will be done for."

"Yes, I know. Our people have tales of her fearsome power, but ever since the fall of Discord, our people have become Nomads, wandering the far reaches of the planet without any one place to call a home."

"Does that mean the Buffalo Kingdom no longer exists?" Twilight asked.

"It exists, but its long since been abandoned." The chief scratched the top of his fuzzy head with his hoof. "Many tribes don't even remember how to get there."

"Anything you can offer Chief Thunderhooves would be of great assistance," Luna told him.

"But shouldn't you know how to get their Princess Luna?" Twilight asked, "You and Celestia created the Elements so…"

"It has been a long time since I stood on a surface that was not the moon, Twilight Sparkle. If the kingdom has fallen, been altered or buried I would not know."

"Then the crystal and its kingdom could remain unguarded to this day, I'd wager. If you know where it originally stood it should still be there."

"Then that is all the assistance we will need," Luna said, strutting towards the train, "Let us go." The other ponies followed Luna in her general direction, but Applejack stayed behind.

She removed her hat and lowered her head, "Chief, if I could make a humble request?"

"Hmm?"

"I can't leave mah friends to do it mahself, else I would, but could y'all let Braeburn and the rest a Appleoosa know what's become of Equestria, just to warn them. I-I don't want to see what happened to Canterlot happen here."

"We'll warn them," Little Strongheart said, stepping forward, "Leave this area to us, Applejack."

Applejack smiled, reassured.

"Applejack, what's the hold up?" Rainbow Dash asked her. "Let's go!"

"Comin!" Applejack called to her blue-coated friend.

"Good luck to you, Applejack."

"You two Chief," Applejack said putting her hat back on her head and galloped back towards the train. "Sorry bout that y'all, wanted to at least take the opportunity to get a message to the town."

"A sentimental effort to be sure, but the sooner we stop my mother the sooner we can protect all of Equestria. If we wait too long," Princess Luna said heading for the cabin, "Nowhere will be safe."

"I understand the urgency!" Applejack shouted, growing incredibly irritable. Fluttershy backed away in fear of Applejack's sudden burst of anger. None of the others knew what brought this on either. "We left so urgently I didn't get to say goodbye to Big Mag, Granny Smith or even my little sis and given what we saw in Canterlot, I'm really worried for them okay? Sorry if my sentimental feelings interfere with this "urgency", but I'm upset and worried can everypony understand that?"

Luna turned around and walked back towards Applejack. She was scowling. "Understand this, fairest Applejack. My sister was robbed from me before my very eyes. I too am gravely upset by what my mother has wrought, but if we stop and warn every place in Equestria we won't stop her in time."

"I-I know…but it's just…" Applejack stared at the floor. Applejack looked at Rarity for support. "Rarity, you get me right, you saw what was goin on in Canterlot. What if her highness does that stuff to your family, your sister especially?"

"She wouldn't **dare!**" Rarity growled like a roaring dragon, becoming protective of her younger sister.

"My mother shows no mercy or discretion towards anypony."

Rarity looked like she was about to attack Luna with unexplained instantly growned sharp fangs and a bloodthirsty pounce as she started to seemingly turn into a ravenous beast.

"All of you stop it!" Twilight exclaimed. The others looked at her. "Look," she said with a serious expression, "We're all worried about our families. I only got to say goodbye to Shining, but my parents _live_ in Canterlot. They're probably already under Queen Nebula's power, but Princess Luna's right. There's nothing we can do. As much as it hurts we have to put our minds past it and focus on our goal. We can't stop Queen Nebula as we are. We are not just Equestria's, but the whole world's last line of defense if we don't stop her and we cannot go back, we cannot stop. We have to know that when things are over that they will go back to the way they were just like with Discord. Is everypony with me on this?"

"I hear you Twi," Applejack said, calming down.

"Me too," Rarity added.

"Good," Twilight then looked to Princess Luna, "Princess, take us up."

"By your command," Luna said and took Twilight and the train up, up and away towards the abandoned kingdom of the Buffalo.

As the group flew overseas for several hours, Rainbow Dash went to see how Applejack was faring as she looked out over the sea with her mane and hat flapping in the breeze.

"Hey, you okay?" Rainbow Dash asked.

"I'm fine RD," Applejack told her.

Rainbow Dash looked out over the ocean with her friend. "You know, I keep trying to put myself in yours and everypony else's hooves, but I can't."

"Whatdya mean?"

"I'm an only child. Sure my parents are still around, but I haven't spoken to them since I flunked out of Flight School and became weather manager. They told me I was squandering my potential and that my desire to join the Wonderbolts was nothing more than chasing an empty dream. So it's just been me and my lonesome."

"But weren't they there to cheer you on at the Equestria young flyers competition? Aren't they at least proud of you for that?"

"Actually…no." Rainbow Dash looked at the ground. "And so…I feel like I really haven't lost anything. You guys are all putting your flanks on the line for ponies that you care about, but the only ponies I really have a connection is nopony besides you all."

Applejack looked up towards the clouds and sun. "I almost wish I was in your hooves."

"Huh?"

"Trust me Rainbow, fightin for someone is great and all, but all the pain and all that worry, the stress it puts on you, it sometimes feels like it ain't worth it, especially if you don't succeed. Sometimes I feel you're lucky that only pony you feel you have to impress is you."

"Heh," Applejack's words seem to make Rainbow Dash feel better as she smiled.

"No come on, what's say we raid the dining cart and see if there ain't somethin we can gather up to eat."

"Sounds good to me," Rainbow Dash said.

In the dining cart there was plenty of food to work with and Pinkie Pie, being one of the better cooks on board, made a scrumptious smorgasbord of sugary, salty and gooey snacks. It was a few more hours before Luna finally lowered the train in front of a large pit of sand out in the middle of nowhere.

"It's not here. Neither the kingdom nor its crystal," Luna noted. "It seems in the last few centuries the kingdom has been buried underneath years of sand and sea water. Rainbow One can thou conjure up a whirlwind to blow this sand completely away?"

"On it!" Rainbow Dash said and flew around in circles to whip up a whirlwind that she used to slowly blow away centuries upon centuries of sand as the old ruin that was once the Buffalo kingdom began to show itself. The kingdom was naught but large, blocky, stone ruins of various shapes and sizes now and it was buried so deep into the surrounding rock coast that by the time Rainbow Dash was done Twilight and the others were now in a 200 foot crater of the same approximate diameter as the group was now in a deep pit.

Twilight looked around. "I don't see the crystal."

"If the crystal were obvious," Luna remarked, "It wouldn't bold well for those that would wish it harm. Come," Luna trotted forward as the others followed behind her towards a far end of the ruined, abandoned city."

"Hard to believe them Buffalo once lived in a grand civilization like this," Applejack stated.

"Yes, I was surprised too to learn that they had become a nomadic tribe upon my return. They were one of the proudest desert civilizations."

"But we're on an island, how did they get to Equestria and the other kingdoms?"

"My wager would be the Griffin Kingdom," Luna stated, "They are good with cross-continental travel."

"Just how long are we going to be down here?" Rarity complained, "This place is filthy!"

"That depends upon fairest Applejack once we reach the crystal," Luna stated.

"Upon me?" Applejack asked.

"You are the embodiment of honesty. The Crystals of Harmony know their bearers and you will face a trial once we reach the crystal itself. You must pass the trial and only then will you be able to become a true embodiment of honesty and be truly worthy of the element you bear."

"What sort of trial will she face?" Twilight asked.

"The trials of the crystal vary from pony to pony, but in their vaguest sense the trials are meant to burrow deep into the heart, mind and soul of the one who would take the trial and force them to overcome a weakness of themselves."

"Weakness?" Rainbow Dash questioned and then added smugly, "I have no weaknesses."

"We shall see, Rainbow One, we shall see," Luna remarked.

The group continued to follow Luna until they entered underneath an archway and then stood in an enclosed space and in front of them was a large, jagged orange crystal that rose up as high as a full grown dragon.

Spike's eyes became the shape of the crystal as he drooled over it and leapt forward to take a bite out of it, but Luna stopped him by pushing down on his back with her hoof, pushing him into the ground. "I would advise against taking a bite out of this crystal, young dragon. See the magic conduits," Luna gestured her hoof forward to show the lightning-like rings of magic running up the crystal all around it. "Only the crystal's bearer may even think about going within immediate distance of the crystal itself. Fairest Applejack, the rest is up to you."

Applejack gulped and then approached with caution. She backed away just a hair's breadth and as she tapped her hoof to the crystal's edge found her hoof entering the crystal as though it was a portal of some kind.

Applejack pulled her hoof back in alarm. "Whoa, check it out!" Rainbow Dash was amazed.

"That is normal," Luna called, "The crystal is meant to be entered by its bearer. Were you not you would've immediately been electrocuted."

"Applejack, we're all here to support you," Twilight told her, "Just do your best."

Applejack put on her toughest look and stepped forward, "All right then, here I go." She walked in fearlessly into the crystal as a bright white light blinded her. When it settled down Applejack soon found herself in the calm, serene meadow in the middle of the acres of Sweet Apple Acres. "What the hay?"

"Applejack!" Applejack looked back to see Applebloom running up to her.

"Applebloom?"

"Applejack you came back! I knew you wouldn't leave behind!"

"Leave you behind, what do you mean?" Applejack asked.

"That Queen Nebula's gone and moved in on Ponyville. She's gonna take over Sweet Apple Acres soon. I was so terrified of her. She already got Sweetie Belle, Scootaloo, Granny Smith and Big Mac. Come on sis, you gotta take me with you. I don't wanna end up like everypony else. She's enslavin' all of the tri-stable area."

Applejack's greatest fear was being tested. She had done exactly this. She had left Applebloom, Granny Smith, and Big Mac behind to Nebula's reign of terror who knew what the high queen would do or was doing to her family. Applejack looked over the horizon and could see a dense crimson fog rolling in and swallowing up Ponyville, coming towards her and her sister.

"Please sis, you gotta take me with you. Are you gonna leave me behind? Don't you care about me?"

Applejack backed up two steps as Applebloom gave her the sad puppy eyes. The crystal's trial had her caught good. What was she supposed to say? If this had occurred, if this was reality, what would she have said to Applebloom? What could she have said to Applebloom? Her sister counted on her, her sister trusted her.

That's when it hit the young mare.

Trust.

Honesty.

That was what was expected of her. She had to be honest, she had to be straightforward. Honesty was her creed. Discord had tried her with this once before of when a lie would hurt less than the truth. But this was different, the crystal was hitting harder to home than Discord ever had and both a lie and either truth of taking her with her or telling her no would hurt. No matter what Applejack did, things wound up against her favor completely.

However, she knew what she had to do. She had to do the honest, responsible thing and made sure Applebloom could still trust her, could still look up to her, and could still love her.

"I can't," Applejack looked at the ground.

"Wh-whu…" Applebloom responded.

"You can't come with me Applebloom, it's too dangerous," Applejack stated, her hat hiding her eyes.

"But if I stay here I'm in just as much danger, I wanna be with you sis!" Applebloom pleaded.

"I know that, but if I took you with me then I'd have to look out for you. I can't have ya jepordizin what needs to be done."

"I won't get in the way! I promise!" Applebloom whined.

"I'm sorry, but that's my decision."

"How could you betray me like this?" Applebloom sniffed.

"I am not betraying you," Applejack picked her head up, showing Applebloom her tears, "When I left, when I actually left I didn't want ta leave ya behind, but I know that I have ta. You just have to trust your reliable older sister that she's gonna fix everything and promise that I'll stop Queen Nebula."

"But what if you don't come back? What if something happens to you while you're gone?"

"I'm made of sterner stuff than that and you know it," Applejack said and removed her hat and put it on Applebloom's head. "There ya go. A promise is a promise and I don't break my promises. I'll come back for real and when I do, I'll be able to protect you, Big Mac, Granny Smith, everypony and me and my friends will stop Queen Nebula in her tracks." Applejack put a hoof around Applebloom and pulled her close. "I'll come back sis, I promise. I love you."

"I love you too, sis. And thanks…for being honest with me."

The world went white around Applejack who then emerged from the crystal with a new necklace of the element of harmony around her neck, a hat of a darker brown with the same gem as her necklace embedded onto the cap and a quartet of boots around each of her hooves complete with spurs and a gem like the element of honesty's gem on either side of each boot.

"Lookin good AJ!"

"I feel good too. I feel like I could buck harder than ever before, run faster than I ever dreamed."

"The gem has bolstered the honesty you possess deep within you as well as your innate abilities. The outfit upon you is a reflection of that. Now the element of honesty's entire power is yours to command."

"So aside from this fancy strength enhancement what's that mean?"

"As from simply sounding fancy not much," Luna admitted.

"Well that's one down and five to go," Twilight stated. "Where to next?"

"To the Griffin Kingdom, it is the closest place to here."

"Yippee! That means I'm next!" Pinkie Pie cheered.

"Indeed it does Pink one," Luna said and then used her magic to smash to teleport the group back to the inside of the train where upon she then lifted the machine up and out of the crater of the abandoned Buffalo Kingdom to the Griffin Kingdom due east.

"The Griffin Kingdom," Rainbow Dash muttered as the magically transformed aircraft took to the skies and zoomed off, "I wonder…if I'll see Gilda."

* * *

**Equestria, Nebula's Throne Room**

Upon her throne, Nebula sat where Celestia normally did so as a messenger/soldier gave her an update on her conquest.

"Your majesty!" he saluted to the queen, "The tri-stable area is completely under your control."

"Excellent," Nebula smiled.

"We still have received no word from the Crystal Kingdom, though your majesty."

"That is problematic," Nebula said, rising to all fours, "Lock my throne room, I have personal business to attend to."

"Yes your majesty," the soldier told her.

Nebula exited her throne room that was locked behind her and went down towards the basement/dungeon of Canterlot castle where upon she had chained up Celestia to the ground. A weighted chain was attached to Celestia's limbs and neck, forcing her to keep her head low to the ground and her body had an anti-magic ring looped around it over her wings and stomach.

Nebula approached her daughter as she stood in front of the cell. Celestia dragged her body towards the front of the cell to greet her mother disdainfully. "What do you want this time?"

"Oh I'm not here for that, but I have a question for you. The Crystal Kingdom is being rather uncooperative. You wouldn't be able to tell me why, would you Celestia darling?"

"Even if I did I wouldn't tell you,"

Nebula's horn lit up and Celestia's chains suddenly shocked the alicorn completely into submission and Celestia collapsed upon the ground.

"I hate it when you resist me, Celestia. I am your mother and you will cow to my authority."

"You're a fowl witch that tyrannically rules over her subjects out of fear that they would turn on her. Father was right to try and stop you. I don't know what he ever saw in you. For as far as I can remember, you have always been like this."

"Except when you changed me to be kind, and cute and cuddly," Nebula reminded her, leering with a gentle, smug smile towards her daughter as she lifted her head up with her hoof and looked Celestia in the eye. "Or are you deliberately forgetting that part?"

"I'll say it again as I did when you first unpetrified me: Luna and the others will stop you. I don't know what you intend to gain by chaining me up. You were better off leaving me a statue."

Nebula pushed up on her daughter's mane with her hoof with the same smug smile on her face, "You have so much faith in your sister that it's cute. I've read all your letters Celestia and I know how you think. And when I tell you that your gambit will fail, you will have to trust me as your mother to know what I'm talking about."

"That's a big line from a wielder of the element of deceit!" Celestia slandered. Nebula's horn glowed again and electrocuted Celestia to her knees. Celestia coughed on the ground.

"You know that you can stop this pain if you choose to join me, Celestia."

"I will never join you. Just as father stood up to you when you transformed Canterlot to what you've done once more, I will never yield either."

"No matter how much pain?"

"Even to death," Celestia glared.

"Then you leave me with no choice," Nebula stated as she loomed over Celestia, wings outspread, "I truly am sorry about this Celestia. A mother should never force her baby to be anything she doesn't want to be, but…if you will not say the words yourself that you will stand at my side, then I will make you."

Celestia then saw a flash of bright crimson light before her self-consciousness faded completely.

**To be continued…**

* * *

**(A/N: Now I think it should be obvious what's going to happen to Celestia, no? At the pace this is going to try and make this a short story fic rather than a full length one (15 chapters as opposed to 30+). I think one chapter per element and then I'm going to have a few chapters for the finale. Let me just say that I already know EXACTLY what I'm going to do for Pinkie Pie and I have SOME idea as for what I'm going to do for Rarity. However, if you have ideas for Rainbow Dash, Fluttershy and Twilight, do let me know and if I like it I might actually use it. After Pinkie Pie the order will be: Fluttershy, Rainbow Dash, Rarity, and Twilight is last. Also if anyone has any guesses as to the "fallen kingdom of magic" do feel free to guess. I already know what it is and I am REALLY looking forward to that reveal. I'm going to get a shower and shaved because I'm growing in a beard and the summer weather is making it really itchy so I'll see you guys maybe in a bit. I might be able to get the next chapter up and out before day's end because I know EXACTLY what I want to do. Ja ne!)**


End file.
